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Author | Huygh, S.; Neyts, E.C. | ||||
Title | Adsorption of C and CHx radicals on anatase (001) and the influence of oxygen vacancies | Type | A1 Journal article | ||
Year | 2015 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
Volume | 119 | Issue | 119 | Pages | 4908-4921 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The adsorption of C and CHx radicals on anatase (001) was studied using DFT within the generalized gradient approximation using the Perde-Burke-Ernzerhof (PBE) functional. We have studied the influence of oxygen vacancies in and at the surface on the adsorption properties of the radicals. For the oxygen vacancies in anatase (001), the most stable vacancy is located at the surface. For this vacancy, the maximal adsorption strength of C and CH decreases compared to the adsorption on the stoichiometric surface, but it increases for CH2 and CH3. If an oxygen vacancy is present in the first subsurface layer, the maximal adsorption strength increases for C, CH, CH2, and CH3. When the vacancy is present in the next subsurface layer, we find that only the CH3 adsorption is enhanced, while the maximal adsorption energies for the other radical species decrease. Not only does the precise location of the oxygen vacancy determine the maximal adsorption interaction, it also influences the adsorption strengths of the radicals at different surface configurations. This determines the probability of finding a certain adsorption configuration at the surface, which in turn influences the possible surface reactions. We find that C preferentially adsorbs far away from the oxygen vacancy, while CH2 and CH3 adsorb preferentially at the oxygen vacancy site. A fraction of CH partially adsorbs at the oxygen vacancy, and another fraction adsorbs further away from the vacancy. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Washington, D.C. | Editor | ||
Language | Wos | 000350840700052 | Publication Date | 2015-02-18 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1932-7447;1932-7455; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.536 | Times cited | 13 | Open Access | |
Notes | Approved | Most recent IF: 4.536; 2015 IF: 4.772 | |||
Call Number | c:irua:124909 | Serial | 63 | ||
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Author | Khalilov, U.; Bogaerts, A.; Neyts, E.C. | ||||
Title | Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors | Type | A1 Journal article | ||
Year | 2015 | Publication | Nature communications | Abbreviated Journal | Nat Commun |
Volume | 6 | Issue | 6 | Pages | 10306 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level. | ||||
Address | PLASMANT research group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium | ||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | English | Wos | 000367584500001 | Publication Date | 2015-12-22 |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2041-1723 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 12.124 | Times cited | 37 | Open Access | |
Notes | The authors gratefully acknowledge financial support from the Fund of Scientific Research Flanders (FWO), Belgium, grant number 12M1315N. The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. We thank Professor Adri C. T. van Duin for sharing the ReaxFF code. | Approved | Most recent IF: 12.124; 2015 IF: 11.470 | ||
Call Number | c:irua:129975 | Serial | 3990 | ||
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Author | Yusupov, M.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A. | ||||
Title | Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments | Type | A1 Journal article | ||
Year | 2017 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
Volume | 7 | Issue | 7 | Pages | 5761 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000405746500072 | Publication Date | 2017-07-12 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.259 | Times cited | 27 | Open Access | OpenAccess |
Notes | M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216 N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. S.R. and S.K. acknowledge funding by the BMBF (FKZ: 03Z2DN12). S.R. acknowledges funding by the Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern (AU 15001). The authors thank M. Hammer for the support and discussion in the biophysical studies and J. Van der Paal for the interesting discussions. | Approved | Most recent IF: 4.259 | ||
Call Number | PLASMANT @ plasmant @ c:irua:144627 | Serial | 4630 | ||
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Author | Marinov, D.; de Marneffe, J.-F.; Smets, Q.; Arutchelvan, G.; Bal, K.M.; Voronina, E.; Rakhimova, T.; Mankelevich, Y.; El Kazzi, S.; Nalin Mehta, A.; Wyndaele, P.-J.; Heyne, M.H.; Zhang, J.; With, P.C.; Banerjee, S.; Neyts, E.C.; Asselberghs, I.; Lin, D.; De Gendt, S. | ||||
Title | Reactive plasma cleaning and restoration of transition metal dichalcogenide monolayers | Type | A1 Journal article | ||
Year | 2021 | Publication | npj 2D Materials and Applications | Abbreviated Journal | npj 2D Mater Appl |
Volume | 5 | Issue | 1 | Pages | 17 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The cleaning of two-dimensional (2D) materials is an essential step in the fabrication of future devices, leveraging their unique physical, optical, and chemical properties. Part of these emerging 2D materials are transition metal dichalcogenides (TMDs). So far there is limited understanding of the cleaning of “monolayer” TMD materials. In this study, we report on the use of downstream H<sub>2</sub>plasma to clean the surface of monolayer WS<sub>2</sub>grown by MOCVD. We demonstrate that high-temperature processing is essential, allowing to maximize the removal rate of polymers and to mitigate damage caused to the WS<sub>2</sub>in the form of sulfur vacancies. We show that low temperature in situ carbonyl sulfide (OCS) soak is an efficient way to resulfurize the material, besides high-temperature H<sub>2</sub>S annealing. The cleaning processes and mechanisms elucidated in this work are tested on back-gated field-effect transistors, confirming that transport properties of WS<sub>2</sub>devices can be maintained by the combination of H<sub>2</sub>plasma cleaning and OCS restoration. The low-damage plasma cleaning based on H<sub>2</sub>and OCS is very reproducible, fast (completed in a few minutes) and uses a 300 mm industrial plasma etch system qualified for standard semiconductor pilot production. This process is, therefore, expected to enable the industrial scale-up of 2D-based devices, co-integrated with silicon technology. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000613258900001 | Publication Date | 2021-01-28 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2397-7132 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | Open Access | OpenAccess | ||
Notes | Daniil Marinov has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 752164. Ekaterina Voronina, Yuri Mankelevitch, and Tatyana Rakhimova are thankful to the Russian Science Foundation (RSF) for financial support (Grant No. 16-12-10361). This study was carried out using the equipment of the shared research facilities of high-performance computing resources at Lomonosov Moscow State University and the computational resources and services of the HPC core facility CalcUA of the University of Antwerp, and VSC (Flemish Supercomputer Center), funded by the Research Foundation-Flanders (FWO) and the Flemish Government. Patrick With gratefully acknowledges imec’s CTO office for financial support during his stay at imec. The authors thank Mr. Surajit Sutar (imec) for his help during sample electrical characterization, and Patrick Verdonck for lab processing. Jean-François de Marneffe thank Prof. Simone Napolitano from the Free University of Brussels for useful discussions on irreversibly adsorbed polymer layers, and Cédric Huyghebaert (imec) for his continuous support in the framework of the Graphene FET Flagship core project. All authors acknowledge the support of imec’s pilot line and materials characterization and analysis (MCA) group, namely Jonathan Ludwig, Stefanie Sergeant, Thomas Nuytten, Olivier Richard, and Thierry Conard. Finally, Daniil Marinov thank Mikhail Krishtab (imec/KU Leuven) for his help in selecting the optimal plasma etch system for this work. Part of this project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 649953. | Approved | Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @c:irua:175871 | Serial | 6671 | ||
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Author | Hoon Park, J.; Kumar, N.; Hoon Park, D.; Yusupov, M.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A.; Ho Kang, M.; Sup Uhm, H.; Ha Choi, E.; Attri, P.; | ||||
Title | A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma | Type | A1 Journal article | ||
Year | 2015 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
Volume | 5 | Issue | 5 | Pages | 13849 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG. | ||||
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Publisher | Nature Publishing Group | Place of Publication | London | Editor | |
Language | Wos | 000360909000001 | Publication Date | 2015-09-09 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2045-2322; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.259 | Times cited | 32 | Open Access | |
Notes | Approved | Most recent IF: 4.259; 2015 IF: 5.578 | |||
Call Number | c:irua:127410 | Serial | 419 | ||
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Author | Khosravian, N.; Kamaraj, B.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations | Type | A1 Journal article | ||
Year | 2016 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
Volume | 6 | Issue | 6 | Pages | 19466 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment. | ||||
Address | Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium | ||||
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Publisher | Place of Publication | Editor | |||
Language | English | Wos | 000369573900001 | Publication Date | 2016-02-09 |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.259 | Times cited | 7 | Open Access | |
Notes | The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number G012413N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen.” | Approved | Most recent IF: 4.259 | ||
Call Number | c:irua:131610 | Serial | 4031 | ||
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Author | Van der Paal, J.; Verheyen, C.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Hampering Effect of Cholesterol on the Permeation of Reactive Oxygen Species through Phospholipids Bilayer: Possible Explanation for Plasma Cancer Selectivity | Type | A1 Journal article | ||
Year | 2017 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
Volume | 7 | Issue | 7 | Pages | 39526 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | In recent years, the ability of cold atmospheric pressure plasmas (CAPS) to selectively induce cell death in cancer cells has been widely established. This selectivity has been assigned to the reactive oxygen and nitrogen species (RONS) created in CAPs. To provide new insights in the search for an explanation for the observed selectivity, we calculate the transfer free energy of multiple ROS across membranes containing a varying amount of cholesterol. The cholesterol fraction is investigated as a selectivity parameter because membranes of cancer cells are known to contain lower fractions of cholesterol compared to healthy cells. We find that cholesterol has a significant effect on the permeation of reactive species across a membrane. Indeed, depending on the specific reactive species, an increasing cholesterol fraction can lead to (i) an increase of the transfer free energy barrier height and width, (ii) the formation of a local free energy minimum in the center of the membrane and (iii) the creation of extra free energy barriers due to the bulky sterol rings. In the context of plasma oncology, these observations suggest that the increased ingress of RONS in cancer cells can be explained by the decreased cholesterol fraction of their cell membrane. |
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000391306900001 | Publication Date | 2017-01-06 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.259 | Times cited | 27 | Open Access | OpenAccess |
Notes | The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number 11U5416N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. | Approved | Most recent IF: 4.259 | ||
Call Number | PLASMANT @ plasmant @ c:irua:139512 | Serial | 4340 | ||
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Author | Schoeters, B.; Neyts, E.C.; Khalilov, U.; Pourtois, G.; Partoens, B. | ||||
Title | Stability of Si epoxide defects in Si nanowires : a mixed reactive force field/DFT study | Type | A1 Journal article | ||
Year | 2013 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
Volume | 15 | Issue | 36 | Pages | 15091-15097 |
Keywords | A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Modeling the oxidation process of silicon nanowires through reactive force field based molecular dynamics simulations suggests that the formation of Si epoxide defects occurs both at the Si/SiOx interface and at the nanowire surface, whereas for flat surfaces, this defect is experimentally observed to occur only at the interface as a result of stress. In this paper, we argue that the increasing curvature stabilizes the defect at the nanowire surface, as suggested by our density functional theory calculations. The latter can have important consequences for the opto-electronic properties of thin silicon nanowires, since the epoxide induces an electronic state within the band gap. Removing the epoxide defect by hydrogenation is expected to be possible but becomes increasingly difficult with a reduction of the diameter of the nanowires. | ||||
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Publisher | Place of Publication | Cambridge | Editor | ||
Language | Wos | 000323520600029 | Publication Date | 2013-07-16 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 1463-9076;1463-9084; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.123 | Times cited | 3 | Open Access | |
Notes | ; BS gratefully acknowledges financial support of the IWT, Institute for the Promotion of Innovation by Science and Technology in Flanders, via the SBO project “SilaSol”. This work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish government and the Universiteit Antwerpen. ; | Approved | Most recent IF: 4.123; 2013 IF: 4.198 | ||
Call Number | UA @ lucian @ c:irua:110793 | Serial | 3130 | ||
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Author | Engelmann, Y.; Bogaerts, A.; Neyts, E.C. | ||||
Title | Thermodynamics at the nanoscale : phase diagrams of nickel-carbon nanoclusters and equilibrium constants for face transitions | Type | A1 Journal article | ||
Year | 2014 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
Volume | 6 | Issue | Pages | 11981-11987 | |
Keywords | A1 Journal article; PLASMANT | ||||
Abstract | Using reactive molecular dynamics simulations, the melting behavior of nickelcarbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickelcarbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method. | ||||
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Publisher | Place of Publication | Cambridge | Editor | ||
Language | Wos | 000343000800049 | Publication Date | 2014-07-24 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 2040-3364;2040-3372; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7.367 | Times cited | 20 | Open Access | |
Notes | Approved | Most recent IF: 7.367; 2014 IF: 7.394 | |||
Call Number | UA @ lucian @ c:irua:119408 | Serial | 3636 | ||
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Author | Engelmann; Bogaerts, A.; Neyts, E.C. | ||||
Title | Thermodynamics at the nanoscale: phase diagrams of nickel-carbon nanoclusters and equilibrium constants for phase transitions | Type | A1 Journal article | ||
Year | 2014 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
Volume | 6 | Issue | 20 | Pages | 11981-11987 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Using reactive molecular dynamics simulations, the melting behavior of nickel-carbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickel-carbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method. | ||||
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Publisher | Place of Publication | Cambridge | Editor | ||
Language | Wos | 000343000800049 | Publication Date | 2014-07-24 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2040-3364;2040-3372; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7.367 | Times cited | 20 | Open Access | |
Notes | Approved | Most recent IF: 7.367; 2014 IF: 7.394 | |||
Call Number | UA @ lucian @ c:irua:121106 | Serial | 3637 | ||
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Author | Ali, S.; Myasnichenko, V.S.; Neyts, E.C. | ||||
Title | Size-dependent strain and surface energies of gold nanoclusters | Type | A1 Journal article | ||
Year | 2016 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
Volume | 18 | Issue | 18 | Pages | 792-800 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Gold nanocluster properties exhibit unique size-dependence. In this contribution, we employ reactive molecular dynamics simulations to calculate the size- and temperature-dependent surface energies, strain energies and atomic displacements for icosahedral, cuboctahedral, truncated octahedral and decahedral Au-nanoclusters. The calculations demonstrate that the surface energy decreases with increasing cluster size at 0 K but increases with size at higher temperatures. The calculated melting curves as a function of cluster size demonstrate the Gibbs-Thomson effect. Atomic displacements and strain are found to strongly depend on the cluster size and both are found to increase with increasing cluster size. These results are of importance for understanding the size-and temperature-dependent surface processes on gold nanoclusters. | ||||
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Publisher | Place of Publication | Cambridge | Editor | ||
Language | Wos | 000369480600017 | Publication Date | 2015-11-18 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.123 | Times cited | 37 | Open Access | |
Notes | Approved | Most recent IF: 4.123 | |||
Call Number | UA @ lucian @ c:irua:131626 | Serial | 4243 | ||
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Author | Van der Paal, J.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A. | ||||
Title | Effect of lipid peroxidation on membrane permeability of cancer and normal cells subjected to oxidative stress | Type | A1 Journal article | ||
Year | 2016 | Publication | Chemical science | Abbreviated Journal | Chem Sci |
Volume | 7 | Issue | 7 | Pages | 489-498 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | We performed molecular dynamics simulations to investigate the effect of lipid peroxidation products on the structural and dynamic properties of the cell membrane. Our simulations predict that the lipid order in a phospholipid bilayer, as a model system for the cell membrane, decreases upon addition of lipid peroxidation products. Eventually, when all phospholipids are oxidized, pore formation can occur. This will allow reactive species, such as reactive oxygen and nitrogen species (RONS), to enter the cell and cause oxidative damage to intracellular macromolecules, such as DNA or proteins. On the other hand, upon increasing the cholesterol fraction of lipid bilayers, the cell membrane order increases, eventually reaching a certain threshold, from which cholesterol is able to protect the membrane against pore formation. This finding is crucial for cancer treatment by plasma technology, producing a large number of RONS, as well as for other cancer treatment methods that cause an increase in the concentration of extracellular RONS. Indeed, cancer cells contain less cholesterol than their healthy counterparts. Thus, they will be more vulnerable to the consequences of lipid peroxidation, eventually enabling the penetration of RONS into the interior of the cell, giving rise to oxidative stress, inducing pro-apoptotic factors. This provides, for the first time, molecular level insight why plasma can selectively treat cancer cells, while leaving their healthy counterparts undamaged, as is indeed experimentally demonstrated. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000366826900058 | Publication Date | 2015-10-16 | |
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ISSN | 2041-6520 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.668 | Times cited | 106 | Open Access | |
Notes | The authors acknowledge nancial support from the Fund for Scientic Research (FWO) Flanders, grant number G012413N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. | Approved | Most recent IF: 8.668 | ||
Call Number | c:irua:131058 | Serial | 3986 | ||
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Author | Khalilov, U.; Bogaerts, A.; Xu, B.; Kato, T.; Kaneko, T.; Neyts, E.C. | ||||
Title | How the alignment of adsorbed ortho H pairs determines the onset of selective carbon nanotube etching | Type | A1 Journal article | ||
Year | 2017 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
Volume | 9 | Issue | 9 | Pages | 1653-1661 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Unlocking the enormous technological potential of carbon nanotubes strongly depends on our ability to specifically produce metallic or semiconducting tubes. While selective etching of both has already been demonstrated, the underlying reasons, however, remain elusive as yet. We here present computational and experimental evidence on the operative mechanisms at the atomic scale. We demonstrate that during the adsorption of H atoms and their coalescence, the adsorbed ortho hydrogen pairs on single-walled carbon nanotubes induce higher shear stresses than axial stresses, leading to the elongation of HC–CH bonds as a function of their alignment with the tube chirality vector, which we denote as the γ-angle. As a result, the C–C cleavage occurs more rapidly in nanotubes containing ortho H-pairs with a small γ-angle. This phenomenon can explain the selective etching of small-diameter semiconductor nanotubes with a similar curvature. Both theoretical and experimental results strongly indicate the important role of the γ-angle in the selective etching mechanisms of carbon nanotubes, in addition to the nanotube curvature and metallicity effects and lead us to clearly understand the onset of selective synthesis/removal of CNT-based materials. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000395422800036 | Publication Date | 2016-12-19 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2040-3364 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7.367 | Times cited | 6 | Open Access | OpenAccess |
Notes | U. K. gratefully acknowledges financial support from the Fund of Scientific Research Flanders (FWO), Belgium (Grant No. 12M1315N). This work was also supported in part by Grant-in- Aid for Young Scientists A (Grant No. 25706028), Grant-in-Aid for Scientific Research on Innovative Areas (Grant No. 26107502) from JSPS KAKENHI. This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. The authors also thank Prof. A. C. T. van Duin for sharing the ReaxFF code and J. Razzokov for his assistance to perform the DFT calculations. | Approved | Most recent IF: 7.367 | ||
Call Number | PLASMANT @ plasmant @ c:irua:140091 | Serial | 4417 | ||
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Author | Dabaghmanesh, S.; Saniz, R.; Neyts, E.; Partoens, B. | ||||
Title | Sulfur-alloyed Cr2O3: a new p-type transparent conducting oxide host | Type | A1 Journal article | ||
Year | 2017 | Publication | RSC advances | Abbreviated Journal | Rsc Adv |
Volume | 7 | Issue | 7 | Pages | 4453-4459 |
Keywords | A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Doped Cr2O3 has been shown to be a p-type transparent conducting oxide (TCO). Its conductivity, however, is low. As for most p-type TCOs, the main problem is the high effective hole mass due to flat valence bands. We use first-principles methods to investigate whether one can increase the valence band dispersion (i.e. reduce the hole mass) by anion alloying with sulfur, while keeping the band gap large enough for transparency. The alloying concentrations considered are given by Cr(4)SxO(6-x), with x = 1-5. To be able to describe the electronic properties of these materials accurately, we first study Cr2O3, examining critically the accuracy of different density functionals and methods, including PBE, PBE+U, HSE06, as well as perturbative approaches within the GW approximation. Our results demonstrate that Cr4S2O4 has an optical band gap of 3.08 eV and an effective hole mass of 1.8 m(e). This suggests Cr4S2O4 as a new p-type TCO host candidate. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000393751300030 | Publication Date | 2017-01-16 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2046-2069 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.108 | Times cited | 9 | Open Access | OpenAccess |
Notes | ; This work was supported by SIM vzw, Technologiepark 935, BE-9052 Zwijnaarde, Belgium, within the InterPoCo project of the H-INT-S horizontal program. The computational resources and services used in this work were provided by the Vlaams Supercomputer Centrum (VSC) and the HPC infrastructure of the University of Antwerp. ; | Approved | Most recent IF: 3.108 | ||
Call Number | UA @ lucian @ c:irua:141543 | Serial | 4528 | ||
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Author | Bal, K.M.; Neyts, E.C. | ||||
Title | Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations | Type | A1 Journal article | ||
Year | 2016 | Publication | Chemical science | Abbreviated Journal | Chem Sci |
Volume | 7 | Issue | 7 | Pages | 5280-5286 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Atomistic simulations can in principle provide an unbiased description of all mechanisms, intermediates, and products of complex chemical processes. However, due to the severe time scale limitation of conventional simulation techniques, unrealistically high simulation temperatures are usually applied, which are a poor approximation of most practically relevant low-temperature applications. In this work, we demonstrate the direct observation at the atomic scale of the pyrolysis and oxidation of n-dodecane at temperatures as low as 700 K through the use of a novel simulation technique, collective variable-driven hyperdynamics (CVHD). A simulated timescale of up to 39 seconds is reached. Product compositions and dominant mechanisms are found to be strongly temperature-dependent, and are consistent with experiments and kinetic models. These simulations provide a first atomic-level look at the full dynamics of the complicated fuel combustion process at industrially relevant temperatures and time scales, unattainable by conventional molecular dynamics simulations. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000380893900059 | Publication Date | 2016-05-05 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2041-6520 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.668 | Times cited | 22 | Open Access | |
Notes | K. M. B. is funded as PhD fellow (aspirant) of the FWO-Flanders (Fund for Scientic Research-Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) and the HPC infrastructure of the University of Antwerp (CalcUA), funded by the Hercules Foundation and the Flemish Government – department EWI. The authors would also like to thank S. Banerjee for assisting with the interpretation of the experimental results. | Approved | Most recent IF: 8.668 | ||
Call Number | c:irua:134577 c:irua:135670 | Serial | 4105 | ||
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Author | Dabaghmanesh, S.; Sarmadian, N.; Neyts, E.C.; Partoens, B. | ||||
Title | A first principles study of p-type defects in LaCrO3 | Type | A1 Journal article | ||
Year | 2017 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
Volume | 19 | Issue | 34 | Pages | 22870-22876 |
Keywords | A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Recently, Sr-doped LaCrO3 has been experimentally introduced as a new p-type transparent conducting oxide. It is demonstrated that substituting Sr for La results in inducing p-type conductivity in LaCrO3. Performing first principles calculations we study the electronic structure and formation energy of various point defects in LaCrO3. Our results for the formation energies show that in addition to Sr, two more divalent defects, Ca and Ba, substituting for La in LaCrO3, behave as shallow acceptors in line with previous experimental reports. We further demonstrate that under oxygen-poor growth conditions, these shallow acceptors will be compensated by intrinsic donor-like defects (an oxygen vacancy and Cr on an oxygen site), but in the oxygen-rich growth regime the shallow acceptors have the lowest formation energies between all considered defects and will lead to p-type conductivity. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Cambridge | Editor | ||
Language | Wos | 000408671600026 | Publication Date | 2017-08-01 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1463-9076; 1463-9084 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.123 | Times cited | 16 | Open Access | OpenAccess |
Notes | ; This work was supported by SIM vzw, Technologiepark 935, BE-9052 Zwijnaarde, Belgium, within the InterPoCo project of the H-INT-S horizontal program. The computational resources and services were provided by the Flemish Supercomputer Center and the HPC infrastructure of the University of Antwerp (CalcUA), both funded by the FWO-Vlaanderen and the Flemish Government. ; | Approved | Most recent IF: 4.123 | ||
Call Number | UA @ lucian @ c:irua:145621 | Serial | 4735 | ||
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Author | Shirazi, M.; Bogaerts, A.; Neyts, E.C. | ||||
Title | A DFT study of H-dissolution into the bulk of a crystalline Ni(111) surface: a chemical identifier for the reaction kinetics | Type | A1 Journal article | ||
Year | 2017 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
Volume | 19 | Issue | 19 | Pages | 19150-19158 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | In this study, we investigated the diffusion of H-atoms to the subsurface and their further diffusion into the bulk of a Ni(111) crystal by means of density functional theory calculations in the context of thermal and plasma-assisted catalysis. The H-atoms at the surface can originate from the dissociative adsorption of H2 or CH4 molecules, determining the surface H-coverage. When a threshold H-coverage is passed, corresponding to 1.00 ML for the crystalline Ni(111) surface, the surface-bound H-atoms start to diffuse to the subsurface. A similar threshold coverage is observed for the interstitial H-coverage. Once the interstitial sites are filled up with a coverage above 1.00 ML of H, dissolution of interstitial H-atoms to the layer below the interstitial sites will be initiated. Hence, by applying a high pressure or inducing a reactive plasma and high temperature, increasing the H-flux to the surface, a large amount of hydrogen can diffuse in a crystalline metal like Ni and can be absorbed. The formation of metal hydride may modify the entire reaction kinetics of the system. Equivalently, the H-atoms in the bulk can easily go back to the surface and release a large amount of heat. In a plasma process, H-atoms are formed in the plasma, and therefore the energy barrier for dissociative adsorption is dismissed, thus allowing achievement of the threshold coverage without applying a high pressure as in a thermal process. As a result, depending on the crystal plane and type of metal, a large number of H-atoms can be dissolved (absorbed) in the metal catalyst, explaining the high efficiency of plasma-assisted catalytic reactions. Here, the mechanism of H-dissolution is established as a chemical identifier for the investigation of the reaction kinetics of a chemical process. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000406334300034 | Publication Date | 2017-06-22 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.123 | Times cited | 10 | Open Access | OpenAccess |
Notes | Financial support from the Reactive Atmospheric Plasma processIng – eDucation (RAPID) network, through the EU 7th Framework Programme (grant agreement no. 606889), is gratefully acknowledged. The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government department (EWI) and the Universiteit Antwerpen. | Approved | Most recent IF: 4.123 | ||
Call Number | PLASMANT @ plasmant @ c:irua:144794 | Serial | 4633 | ||
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Author | Bal, K.M.; Neyts, E.C. | ||||
Title | Modelling molecular adsorption on charged or polarized surfaces: a critical flaw in common approaches | Type | A1 Journal article | ||
Year | 2018 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
Volume | 20 | Issue | 13 | Pages | 8456-8459 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | A number of recent computational material design studies based on density functional theory (DFT) calculations have put forward a new class of materials with electrically switchable chemical characteristics that can be exploited in the development of tunable gas storage and electrocatalytic applications. We find systematic flaws in almost every computational study of gas adsorption on polarized or charged surfaces, stemming from an improper and unreproducible treatment of periodicity, leading to very large errors of up to 3 eV in some cases. Two simple corrective procedures that lead to consistent results are proposed, constituting a crucial course correction to the research in the field. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000428779700007 | Publication Date | 2018-03-12 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.123 | Times cited | 8 | Open Access | OpenAccess |
Notes | K. M. B. is funded as PhD fellow (aspirant) of the FWO-Flanders (Research Foundation – Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government – department EWI. | Approved | Most recent IF: 4.123 | ||
Call Number | PLASMANT @ plasmant @c:irua:150357 | Serial | 4916 | ||
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Author | Aussems, D.U.B.; Bal, K. M.; Morgan, T.W.; van de Sanden, M.C.M.; Neyts, E.C. | ||||
Title | Atomistic simulations of graphite etching at realistic time scales | Type | A1 Journal article | ||
Year | 2017 | Publication | Chemical science | Abbreviated Journal | Chem Sci |
Volume | 8 | Issue | 10 | Pages | 7160-7168 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Hydrogen–graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe timescale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of 1020 m2 s1. The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C–C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching – chemical erosion – is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed. |
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000411730500055 | Publication Date | 2017-08-24 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2041-6520 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.668 | Times cited | 3 | Open Access | OpenAccess |
Notes | DIFFER is part of the Netherlands Organisation for Scientic Research (NWO). K. M. B. is funded as a PhD fellow (aspirant) of the FWO-Flanders (Fund for Scientic Research-Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI. | Approved | Most recent IF: 8.668 | ||
Call Number | PLASMANT @ plasmant @c:irua:145519 | Serial | 4707 | ||
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Author | Khalilov, U.; Vets, C.; Neyts, E.C. | ||||
Title | Molecular evidence for feedstock-dependent nucleation mechanisms of CNTs | Type | A1 Journal article | ||
Year | 2019 | Publication | Nanoscale Horizons | Abbreviated Journal | Nanoscale Horiz. |
Volume | 4 | Issue | 3 | Pages | 674-682 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Atomic scale simulations have been shown to be a powerful tool for elucidating the growth mechanisms of carbon nanotubes. The growth picture is however not entirely clear yet due to the gap between current simulations and real experiments. We here simulate for the first time the nucleation and subsequent growth of single-wall carbon nanotubes (SWNTs) from oxygen-containing hydrocarbon feedstocks using the hybrid Molecular Dynamics/Monte Carlo technique. The underlying nucleation mechanisms of Ni-catalysed SWNT growth are discussed in detail. Specifically, we find that as a function of the feedstock, different carbon fractions may emerge as the main growth species, due to a competition between the feedstock decomposition, its rehydroxylation and its contribution to etching of the growing SWNT. This study provides a further understanding of the feedstock effects in SWNT growth in comparison with available experimental evidence as well as with<italic>ab initio</italic>and other simulation data, thereby reducing the simulation–experiment gap. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000471816500011 | Publication Date | 2019-01-02 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2055-6756 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | 1 | Open Access | Not_Open_Access: Available from 03.01.2020 | |
Notes | Fonds Wetenschappelijk Onderzoek, 12M1318N 1S22516N ; The authors gratefully acknowledge financial support from the Research Foundation Flanders (FWO), Belgium (Grant numbers 12M1318N and 1S22516N). The work was carried out in part using the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by FWO and the Flemish Government (Department EWI). We thank Prof. A. C. T. van Duin for sharing the reax-code and forcefield parameters. | Approved | Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:159658 | Serial | 5169 | ||
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Author | Heyne, M.H.; de Marneffe, J.-F.; Nuytten, T.; Meersschaut, J.; Conard, T.; Caymax, M.; Radu, I.; Delabie, A.; Neyts, E.C.; De Gendt, S. | ||||
Title | The conversion mechanism of amorphous silicon to stoichiometric WS2 | Type | A1 Journal article | ||
Year | 2018 | Publication | Journal of materials chemistry C : materials for optical and electronic devices | Abbreviated Journal | J Mater Chem C |
Volume | 6 | Issue | 15 | Pages | 4122-4130 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The deposition of ultra-thin tungsten films and their related 2D chalcogen compounds on large area dielectric substrates by gas phase reactions is challenging. The lack of nucleation sites complicates the adsorption of W-related precursors and subsequent sulfurization usually requires high temperatures. We propose here a technique in which a thin solid amorphous silicon film is used as reductant for the gas phase precursor WF6 leading to the conversion to metallic W. The selectivity of the W conversion towards the underlying dielectric surfaces is demonstrated. The role of the Si surface preparation, the conversion temperature, and Si thickness on the formation process is investigated. Further, the in situ conversion of the metallic tungsten into thin stoichiometric WS2 is achieved by a cyclic approach based on WF6 and H2S pulses at the moderate temperature of 450 1C, which is much lower than usual oxide sulfurization processes. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000430538000036 | Publication Date | 2018-03-20 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2050-7526 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 5.256 | Times cited | 4 | Open Access | OpenAccess |
Notes | This work was supported throughout a strategic fundamental research grant for M. H. by the agency Flanders innovation & entrepreneurship (VLAIO). | Approved | Most recent IF: 5.256 | ||
Call Number | PLASMANT @ plasmant @c:irua:150968 | Serial | 4921 | ||
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Author | Izadi, M.E.; Bal, K.M.; Maghari, A.; Neyts, E.C. | ||||
Title | Reaction mechanisms of C(3PJ) and C+(2PJ) with benzene in the interstellar medium from quantum mechanical molecular dynamics simulations | Type | A1 Journal article | ||
Year | 2021 | Publication | Physical Chemistry Chemical Physics | Abbreviated Journal | Phys Chem Chem Phys |
Volume | 23 | Issue | 7 | Pages | 4205-4216 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | While spectroscopic data on small hydrocarbons in interstellar media in combination with crossed molecular beam (CMB) experiments have provided a wealth of information on astrochemically relevant species, much of the underlying mechanistic pathways of their formation remain elusive. Therefore, in this work, the chemical reaction mechanisms of C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>and C<sup>+</sup>(<sup>2</sup>P) + C<sub>6</sub>H<sub>6</sub>systems using the quantum mechanical molecular dynamics (QMMD) technique at the PBE0-D3(BJ) level of theory is investigated, mimicking a CMB experiment. Both the dynamics of the reactions as well as the electronic structure for the purpose of the reaction network are evaluated. The method is validated for the first reaction by comparison to the available experimental data. The reaction scheme for the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system covers the literature data,<italic>e.g.</italic>the major products are the 1,2-didehydrocycloheptatrienyl radical (C<sub>7</sub>H<sub>5</sub>) and benzocyclopropenyl radical (C<sub>6</sub>H<sub>5</sub>–CH), and it reveals the existence of less common pathways for the first time. The chemistry of the C<sup>+</sup>(<sup>2</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system is found to be much richer, and we have found that this is because of more exothermic reactions in this system in comparison to those in the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system. Moreover, using the QMMD simulation, a number of reaction paths have been revealed that produce three distinct classes of reaction products with different ring sizes. All in all, at all the collision energies and orientations, the major product is the heptagon molecular ion for the ionic system. It is also revealed that the collision orientation has a dominant effect on the reaction products in both systems, while the collision energy mostly affects the charged system. These simulations both prove the applicability of this approach to simulate crossed molecular beams, and provide fundamental information on reactions relevant for the interstellar medium. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000621595300016 | Publication Date | 2021-01-18 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.123 | Times cited | Open Access | OpenAccess | |
Notes | Fonds Wetenschappelijk Onderzoek, 12ZI420N ; Ministry of Science Research and Technology; Universiteit Antwerpen; The financial support from the Iran Ministry of Science, Research and Technology and PLASMANT Research Group University of Antwerp is highly acknowledged by the authors. K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation – Flanders), Grant 12ZI420N. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. | Approved | Most recent IF: 4.123 | ||
Call Number | PLASMANT @ plasmant @c:irua:176672 | Serial | 6742 | ||
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Author | Grubova, I.Y.; Surmeneva, M.A.; Surmenev, R.A.; Neyts, E.C. | ||||
Title | Effect of van der Waals interactions on the adhesion strength at the interface of the hydroxyapatite-titanium biocomposite : a first-principles study | Type | A1 Journal article | ||
Year | 2020 | Publication | RSC advances | Abbreviated Journal | |
Volume | 10 | Issue | 62 | Pages | 37800-37805 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Hydroxyapatite (HAP) is frequently used as biocompatible coating on Ti-based implants. In this context, the HAP-Ti adhesion is of crucial importance. Here, we report ab initio calculations to investigate the influence of Si incorporation into the amorphous calcium-phosphate (a-HAP) structure on the interfacial bonding mechanism between the a-HAP coating and an amorphous titanium dioxide (a-TiO2) substrate, contrasting two different density functionals: PBE-GGA, and DFT-D3, which are capable of describing the influence of the van der Waals (vdW) interactions. In particular, we discuss the effect of dispersion on the work of adhesion (W-ad), equilibrium geometries, and charge density difference (CDD). We find that replacement of P by Si in a-HAP (a-Si-HAP) with the creation of OH vacancies as charge compensation results in a significant increase in the bond strength between the coating and substrate in the case of using the PBE-GGA functional. However, including the vdW interactions shows that these forces considerably contribute to the W-ad. We show that the difference (W-ad – W-ad(vdW)) is on average more than 1.1 J m(-2) and 0.5 J m(-2) for a-HAP/a-TiO2 and a-Si-HAP/a-TiO2, respectively. These results reveal that including vdW interactions is essential for accurately describing the chemical bonding at the a-HAP/a-TiO2 interface. | ||||
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Language | Wos | 000583523300025 | Publication Date | 2020-10-14 | |
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ISSN | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | ||
Impact Factor | Times cited | Open Access | |||
Notes | ; The authors gratefully acknowledge financial support from the Russian president's grant MK-330.2020.8 and BOF Fellowships for International Joint PhD students funded by University of Antwerp (UAntwerp, project number 32545). The work was carried out at Tomsk Polytechnic University within the framework of Tomsk Polytechnic University Competitiveness Enhancement Program grant and in part using the Turing HPC infrastructure of the CalcUA core facility of the UAntwerp, a division of the Flemish Supercomputer Centre (VSC), funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerp, Belgium. ; | Approved | Most recent IF: NA | ||
Call Number | UA @ admin @ c:irua:173603 | Serial | 6499 | ||
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Author | Faraji, F.; Neek-Amal, M.; Neyts, E.C.; Peeters, F.M. | ||||
Title | Indentation of graphene nano-bubbles | Type | A1 Journal article | ||
Year | 2022 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
Volume | 14 | Issue | 15 | Pages | 5876-5883 |
Keywords | A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Molecular dynamics simulations are used to investigate the effect of an AFM tip when indenting graphene nano bubbles filled by a noble gas (i.e. He, Ne and Ar) up to the breaking point. The failure points resemble those of viral shells as described by the Foppl-von Karman (FvK) dimensionless number defined in the context of elasticity theory of thin shells. At room temperature, He gas inside the bubbles is found to be in the liquid state while Ne and Ar atoms are in the solid state although the pressure inside the nano bubble is below the melting pressure of the bulk. The trapped gases are under higher hydrostatic pressure at low temperatures than at room temperature. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000776763000001 | Publication Date | 2022-03-30 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2040-3364; 2040-3372 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 6.7 | Times cited | 2 | Open Access | OpenAccess |
Notes | Approved | Most recent IF: 6.7 | |||
Call Number | UA @ admin @ c:irua:187924 | Serial | 7171 | ||
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Author | Bal, K.M.; Neyts, E.C. | ||||
Title | On the time scale associated with Monte Carlo simulations | Type | A1 Journal article | ||
Year | 2014 | Publication | The journal of chemical physics | Abbreviated Journal | J Chem Phys |
Volume | 141 | Issue | 20 | Pages | 204104 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | New York, N.Y. | Editor | ||
Language | Wos | 000345641400005 | Publication Date | 2014-11-26 | |
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ISSN | 0021-9606;1089-7690; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.965 | Times cited | 26 | Open Access | |
Notes | Approved | Most recent IF: 2.965; 2014 IF: 2.952 | |||
Call Number | UA @ lucian @ c:irua:120667 | Serial | 2459 | ||
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Author | Dumpala, S.; Broderick, S.R.; Khalilov, U.; Neyts, E.C.; van Duin, A.C.T.; Provine, J.; Howe, R.T.; Rajan, K. | ||||
Title | Integrated atomistic chemical imaging and reactive force field molecular dynamic simulations on silicon oxidation | Type | A1 Journal article | ||
Year | 2015 | Publication | Applied physics letters | Abbreviated Journal | Appl Phys Lett |
Volume | 106 | Issue | 106 | Pages | 011602 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO2 and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature. | ||||
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Publisher | American Institute of Physics | Place of Publication | New York, N.Y. | Editor | |
Language | Wos | 000347976900008 | Publication Date | 2015-01-06 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0003-6951;1077-3118; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.411 | Times cited | 19 | Open Access | |
Notes | Approved | Most recent IF: 3.411; 2015 IF: 3.302 | |||
Call Number | c:irua:122300 | Serial | 1679 | ||
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Author | Bal, K.M.; Fukuhara, S.; Shibuta, Y.; Neyts, E.C. | ||||
Title | Free energy barriers from biased molecular dynamics simulations | Type | A1 Journal article | ||
Year | 2020 | Publication | Journal Of Chemical Physics | Abbreviated Journal | J Chem Phys |
Volume | 153 | Issue | 11 | Pages | 114118 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000574665600004 | Publication Date | 2020-09-21 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0021-9606 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.4 | Times cited | Open Access | ||
Notes | Japan Society for the Promotion of Science, 19H02415 18J22727 ; Fonds Wetenschappelijk Onderzoek, 12ZI420N ; This work was supported, in part, by a Grant-in-Aid for Scientific Research (B) (Grant No. 19H02415) and Grant-in-Aid for a JSPS Research Fellow (Grant No. 18J22727) from the Japan Society for the Promotion of Science (JSPS), Japan. K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation – Flanders), Grant No. 12ZI420N. S.F. was supported by JSPS through the Program for Leading Graduate Schools (MERIT). The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. The authors are grateful to Pablo Piaggi for making the pair entropy CV code publicly available. | Approved | Most recent IF: 4.4; 2020 IF: 2.965 | ||
Call Number | PLASMANT @ plasmant @c:irua:172456 | Serial | 6420 | ||
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Author | Bal, K.M.; Neyts, E.C. | ||||
Title | Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory | Type | A1 Journal article | ||
Year | 2022 | Publication | Journal Of Chemical Physics | Abbreviated Journal | J Chem Phys |
Volume | 157 | Issue | 18 | Pages | 184113-10 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000885260600002 | Publication Date | 2022-11-14 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0021-9606 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.4 | Times cited | Open Access | OpenAccess | |
Notes | Approved | Most recent IF: 4.4 | |||
Call Number | UA @ admin @ c:irua:192076 | Serial | 7266 | ||
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Author | Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine | Type | A1 Journal article | ||
Year | 2015 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 48 | Issue | 48 | Pages | 155202 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function. | ||||
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Publisher | Place of Publication | London | Editor | ||
Language | Wos | 000351856600007 | Publication Date | 2015-03-25 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0022-3727;1361-6463; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.588 | Times cited | 20 | Open Access | |
Notes | Approved | Most recent IF: 2.588; 2015 IF: 2.721 | |||
Call Number | c:irua:124230 | Serial | 3242 | ||
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Author | Tinck, S.; Tillocher, T.; Dussart, R.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Elucidating the effects of gas flow rate on an SF6inductively coupled plasma and on the silicon etch rate, by a combined experimental and theoretical investigation | Type | A1 Journal article | ||
Year | 2016 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 49 | Issue | 49 | Pages | 385201 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Experiments show that the etch rate of Si with SF6 inductively coupled plasma (ICP) is significantly influenced by the absolute gas flow rate in the range of 50–600 sccm, with a maximum at around 200 sccm. Therefore, we numerically investigate the effects of the gas flow rate on the bulk plasma properties and on the etch rate, to obtain more insight in the underlying reasons of this effect. A hybrid Monte Carlo—fluid model is applied to simulate an SF6 ICP. It is found that the etch rate is influenced by two simultaneous effects: (i) the residence time of the gas and (ii) the temperature profile of the plasma in the ICP volume, resulting indeed in a maximum etch rate at 200 sccm. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000384095900011 | Publication Date | 2016-08-24 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0022-3727 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.588 | Times cited | 1 | Open Access | |
Notes | We are very grateful to Mark Kushner for providing the computational model. The Fund for Scientific Research Flanders (FWO; grant no. 0880.212.840) is acknowledged for financial support of this work. The work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the University of Antwerp. | Approved | Most recent IF: 2.588 | ||
Call Number | c:irua:134867 | Serial | 4108 | ||
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